Contacts of the strand formed by residues 1046 - 1058 (chain I) in PDB entry 6ASX


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with VAL1046 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    839I  VAL*     4.1     8.7    -      -       +      -
    840I  SER      3.4    31.0    -      -       -      +
    841I  ARG*     4.0    16.4    -      -       +      +
    936I  ARG*     3.9    14.9    +      -       -      -
   1042I  LEU*     3.8    24.3    -      -       +      +
   1043I  ALA*     3.4    29.6    -      -       +      +
   1044I  PRO      3.5     2.2    +      -       -      +
   1045I  GLY*     1.3    79.4    +      -       -      +
   1047I  LEU*     1.3    67.1    +      -       -      +
   1048I  LYS      3.9     8.3    -      -       -      +
   1049I  ILE*     4.0    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU1047 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    840I  SER*     2.9    17.8    +      -       -      +
    841I  ARG      5.1     1.1    -      -       -      +
    842I  ASP*     4.4    22.0    -      -       +      +
    847I  PRO*     4.5    16.8    -      -       +      -
    848I  GLU      5.6     3.1    -      -       -      +
    935I  THR*     4.0     0.3    -      -       -      -
    936I  ARG*     2.9    47.4    +      -       +      +
    938I  GLY      6.1     1.3    -      -       -      +
    939I  VAL*     4.2    21.9    -      -       +      +
   1042I  LEU*     3.6     4.7    -      -       -      -
   1045I  GLY      4.2     9.2    -      -       -      +
   1046I  VAL*     1.3    83.1    -      -       -      +
   1048I  LYS*     1.3    67.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS1048 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    838I  CYS      4.4     0.7    -      -       -      +
    839I  VAL      3.9     0.5    -      -       -      -
    840I  SER*     3.2    40.0    +      -       -      +
    850I  ILE*     3.7    29.2    -      -       +      +
    933I  VAL*     5.2     4.7    -      -       +      -
    934I  PHE      3.1    15.3    -      -       -      +
    935I  THR*     4.7     2.5    -      -       -      -
    939I  VAL*     4.5    18.2    -      -       -      +
    940I  GLU      4.3     5.9    +      -       -      -
    941I  LYS*     3.4    39.0    -      -       +      +
   1042I  LEU*     4.0     2.6    -      -       -      +
   1046I  VAL*     3.9     0.5    -      -       -      +
   1047I  LEU*     1.3    80.4    -      -       +      +
   1049I  ILE*     1.3    65.9    -      -       -      +
   1050I  VAL*     5.1    11.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE1049 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    837I  ALA*     5.2     3.1    -      -       +      -
    838I  CYS      4.1     5.8    -      -       -      +
    839I  VAL*     3.8    29.8    -      -       +      -
    932I  GLN      3.8     0.7    -      -       -      +
    933I  VAL*     3.5     1.9    -      -       -      -
    934I  PHE*     2.9    51.8    +      -       +      +
   1042I  LEU*     3.9    21.7    -      -       +      +
   1043I  ALA*     6.3     1.3    -      -       +      -
   1046I  VAL*     4.0    14.6    -      -       +      -
   1048I  LYS*     1.3    77.9    -      -       -      +
   1050I  VAL*     1.3    67.4    +      -       -      +
   1051I  LYS*     4.2    25.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL1050 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    837I  ALA*     3.7     1.9    -      -       -      -
    838I  CYS*     3.0    38.1    +      -       -      +
    850I  ILE*     4.7    19.5    -      -       +      -
    870I  ILE*     4.4    12.3    -      -       +      -
    884I  VAL*     3.8    28.3    -      -       +      +
    918I  LEU*     5.5     0.5    -      -       -      +
    931I  VAL*     4.3    12.8    -      -       +      -
    932I  GLN      3.3     8.1    -      -       -      +
    933I  VAL*     3.8    23.1    -      -       +      -
   1048I  LYS*     4.3     8.9    -      -       +      -
   1049I  ILE*     1.3    77.1    -      -       -      +
   1051I  LYS*     1.3    68.7    +      -       -      +
   1052I  VAL*     4.3     2.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with LYS1051 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87I  ILE      5.7     0.4    +      -       -      -
     88I  ARG      5.5     1.8    +      -       -      -
    835I  GLU*     3.4    28.0    +      -       +      +
    836I  LEU      3.3    12.6    -      -       -      +
    837I  ALA*     4.6     9.0    -      -       +      -
    930I  ASP      4.1     0.3    -      -       -      +
    931I  VAL*     3.4     6.1    -      -       -      +
    932I  GLN*     2.9    43.5    +      -       +      +
    934I  PHE*     4.0    28.5    -      -       +      -
   1049I  ILE*     4.0    17.9    +      -       +      -
   1050I  VAL*     1.3    77.1    -      -       -      +
   1052I  VAL*     1.3    64.1    +      -       -      +
   1053I  TYR*     4.3    11.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL1052 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    835I  GLU*     3.9     0.4    -      -       -      -
    836I  LEU*     3.0    37.2    +      -       +      +
    870I  ILE*     5.0     1.6    -      -       +      -
    871I  VAL*     4.4    10.1    -      -       +      -
    883I  LEU*     3.8    28.5    -      -       +      -
    884I  VAL*     4.2    24.2    -      -       +      -
    918I  LEU*     5.5     1.8    -      -       +      +
    928I  VAL*     3.7    22.4    -      -       +      -
    930I  ASP      3.8     2.7    -      -       -      -
    931I  VAL*     4.1    13.2    -      -       +      -
   1050I  VAL*     4.3     5.1    +      -       +      -
   1051I  LYS*     1.3    79.2    -      -       -      +
   1053I  TYR*     1.3    75.0    +      -       -      +
   1054I  LEU*     4.0     2.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR1053 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    757I  THR*     5.7     3.8    -      -       -      -
    758I  ARG*     4.1    14.1    -      -       +      -
    833I  ILE*     4.3    11.9    -      -       +      -
    834I  GLN      3.5    16.8    -      -       -      +
    835I  GLU*     3.5    39.2    +      -       +      -
    928I  VAL*     3.4    22.3    -      -       -      +
    929I  ILE*     4.2    18.2    -      -       +      -
    930I  ASP*     3.0    47.6    +      -       +      +
    932I  GLN*     4.1    18.8    -      -       +      +
   1051I  LYS*     4.7     9.6    +      -       +      +
   1052I  VAL*     1.3    80.4    -      -       -      +
   1054I  LEU*     1.3    66.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU1054 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    833I  ILE*     3.3     5.8    -      -       -      +
    834I  GLN*     2.8    43.1    +      -       +      +
    836I  LEU*     3.8    26.9    -      -       +      -
    877I  VAL*     3.8    22.9    -      -       +      -
    883I  LEU*     4.0    20.4    -      -       +      -
    920I  VAL*     4.6    15.3    -      -       +      -
    924I  VAL*     5.1     4.0    -      -       +      -
    925I  SER      3.4    27.1    -      -       -      +
    926I  GLY*     4.4     1.8    -      -       -      -
    927I  THR      3.8     5.8    -      -       -      +
    928I  VAL*     4.5     9.6    -      -       +      -
    929I  ILE*     5.2     0.7    -      -       -      -
   1052I  VAL*     4.0     5.4    -      -       +      +
   1053I  TYR*     1.3    82.3    -      -       -      +
   1055I  ALA*     1.3    61.3    +      -       -      +
   1056I  VAL*     4.1     2.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA1055 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68G  TYR*     4.2    24.1    +      -       +      -
    831I  ILE*     5.2     2.5    -      -       +      -
    832I  HIS      3.5     8.5    -      -       -      +
    833I  ILE*     4.2    12.3    -      -       +      -
    926I  GLY*     3.3     3.3    -      -       -      -
    927I  THR*     3.2    35.9    +      -       -      +
    929I  ILE*     3.9    20.6    -      -       +      -
   1054I  LEU*     1.3    73.7    -      -       -      +
   1056I  VAL*     1.3    62.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL1056 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68G  TYR*     4.7     2.0    -      -       -      -
    831I  ILE*     3.8     3.1    -      -       -      +
    832I  HIS*     2.8    36.1    +      -       +      +
    834I  GLN*     5.0    14.8    -      -       +      +
    925I  SER*     3.3    42.8    -      -       -      +
    926I  GLY*     3.9     2.0    -      -       -      -
   1054I  LEU*     4.9     3.8    -      -       +      +
   1055I  ALA*     1.3    78.8    -      -       -      +
   1057I  LYS*     1.3    64.5    +      -       -      +
   1058I  ARG*     3.7    44.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS1057 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67G  GLU*     4.2    17.1    +      -       -      -
     68G  TYR*     3.7    24.9    +      -       -      +
     79G  LEU*     4.2    23.2    -      -       -      +
     82G  LEU*     6.3     0.2    -      -       -      +
     83G  LEU*     5.8     3.0    -      -       -      +
    693I  LEU*     4.6    12.3    -      -       -      +
    826I  ASP*     6.4     0.2    -      -       -      -
    829I  THR*     3.6    28.3    -      -       +      -
    830I  THR      3.9     7.6    -      -       -      +
    831I  ILE*     4.6     9.0    -      -       +      +
   1055I  ALA      4.3     0.6    +      -       -      -
   1056I  VAL*     1.3    76.4    -      -       -      +
   1058I  ARG*     1.3    61.4    +      -       -      +
   1059I  ARG*     4.0    30.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG1058 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    829I  THR*     4.6     0.7    -      -       -      -
    830I  THR*     3.2    30.6    +      -       +      +
    832I  HIS*     3.3    37.6    +      -       +      +
    834I  GLN*     4.5    17.8    -      -       -      +
    924I  VAL*     5.0    11.1    -      -       -      +
    925I  SER      5.7     0.2    -      -       -      +
   1056I  VAL*     3.7    38.5    +      -       +      +
   1057I  LYS*     1.3    73.5    -      -       -      +
   1059I  ARG*     1.3    67.0    +      -       -      +
   1061I  GLN*     6.0     1.8    -      -       -      +
   1234I  LYS*     4.0     0.6    +      -       -      -
   1238I  LEU*     3.9    18.2    -      -       +      -
   1240I  ASP*     3.0    40.9    +      -       -      +
   1241I  ASP*     4.5    13.9    +      -       -      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il